State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China.
Yunnan Key Laboratory of Stem Cell and Regenerative Medicine & Biomedical Engineering Research Center, Kunming Medical University, Kunming 650500, China.
Int J Mol Sci. 2021 Feb 11;22(4):1781. doi: 10.3390/ijms22041781.
Cold-adapted enzymes feature a lower thermostability and higher catalytic activity compared to their warm-active homologues, which are considered as a consequence of increased flexibility of their molecular structures. The complexity of the (thermo)stability-flexibility-activity relationship makes it difficult to define the strategies and formulate a general theory for enzyme cold adaptation. Here, the psychrophilic serine hydroxymethyltransferase (pSHMT) from and its mesophilic counterpart, mSHMT from , were subjected to μs-scale multiple-replica molecular dynamics (MD) simulations to explore the cold-adaptation mechanism of the dimeric SHMT. The comparative analyses of MD trajectories reveal that pSHMT exhibits larger structural fluctuations and inter-monomer positional movements, a higher global flexibility, and considerably enhanced local flexibility involving the surface loops and active sites. The largest-amplitude motion mode of pSHMT describes the trends of inter-monomer dissociation and enlargement of the active-site cavity, whereas that of mSHMT characterizes the opposite trends. Based on the comparison of the calculated structural parameters and constructed free energy landscapes (FELs) between the two enzymes, we discuss in-depth the physicochemical principles underlying the stability-flexibility-activity relationships and conclude that (i) pSHMT adopts the global-flexibility mechanism to adapt to the cold environment and, (ii) optimizing the protein-solvent interactions and loosening the inter-monomer association are the main strategies for pSHMT to enhance its flexibility.
与温暖活性同系物相比,冷适应酶的热稳定性较低,催化活性较高,这被认为是其分子结构柔韧性增加的结果。(热)稳定性-柔韧性-活性关系的复杂性使得难以定义酶冷适应的策略和制定一般理论。在这里,来自 和其嗜温对应物 mSHMT 来自 的嗜冷丝氨酸羟甲基转移酶 (pSHMT) 被进行了微秒级别的多复制分子动力学 (MD) 模拟,以探索二聚 SHMT 的冷适应机制。MD 轨迹的比较分析表明,pSHMT 表现出更大的结构波动和单体间的位置运动,更高的整体柔韧性,以及明显增强的涉及表面环和活性位点的局部柔韧性。pSHMT 的最大幅度运动模式描述了单体间解离和活性位点腔增大的趋势,而 mSHMT 的运动模式则相反。基于两种酶之间计算的结构参数和构建的自由能景观 (FEL) 的比较,我们深入讨论了稳定性-柔韧性-活性关系背后的物理化学原理,并得出结论:(i) pSHMT 采用整体柔韧性机制来适应寒冷环境,和 (ii) 优化蛋白质-溶剂相互作用和松开单体间的缔合是 pSHMT 增强其柔韧性的主要策略。